Eddington commanded Deep Space 9 when Benjamin Sisko and other senior officers were at a conference. After Sisko and the others' patterns did not materialize, Eddington had the computer store them elsewhere before they degraded. Eddington later worked with Rom and Odo to reintegrate the senior officers. (DS9episode: "Our Man Bashir")

Later in 2373, Rebecca Sullivan, Eddington's wife, sent a general message to Eddington informing him they had launched the cloaked missiles against Cardassia. The missiles did not exist, but were a code to tell him they had reached their safehouse on Athos IV. Sisko, believing Eddington could disarm the missiles from Athos, brought Eddington there, but soon discovered the missile story had been faked. To give Sisko time to evacuate Sullivan and the other Maquis survivors, Eddington engaged several Jem'Hadar in a phaser battle and was killed. His last word was his wife's name. (DS9episode: "Blaze of Glory")

In an alternate reality, Eddington served in the command division aboard Deep Space 9 in 2371 but still worked for station security. That year, Federation and Dominion delegations met on DS9 to negotiate a treaty in response to the Dominion's peace overtures. However, during the talks, Odo was murdered with a phaser. Consequently, the negotiations broke down and the Dominion launched an attack on DS9. Although the Federation forces were eventually able to push the Jem'Hadar back through the Bajoran wormhole, DS9 suffered significant damage and heavy casualties. However, before retreating through the wormhole, the Dominion were able to capture CommanderBenjamin Sisko, DoctorJulian Bashir and MajorKira Nerys. Odo's death left Eddington in charge of security aboard DS9 while Sisko's kidnapping made him the station's de factocommanding officer.

While posing as his murdered counterpart, the Odo of the primary universe accused Eddington of staging the attack on him. Odo argued that Eddington would never attain the position of security chief while he was still alive and commented that, although everyone assumed that the attack on him was politically motivation, it could have been personal. Eddington told Odo that he would not dignify the accusation with a response. Odo later determined that the alternate MajorKira Nerys was responsible for killing the other Odo as she feared the consequences for Bajor if the Federation and Bajor were to form an alliance. (DS9comic: "The Looking Glass War")